Susceptibility of spike glycoprotein and RNA-dependent RNA polymerase of SARS-CoV-2 to mutation: in silico structural dynamics study

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a pathogen that causes coronavirus disease 2019 (COVID-19) which was first recorded at Wuhan city, China in December 2019, and it has caused 262,866,050 confirmed cases which has resulted to over 5,224,519 deaths worldwide as of 3 December 2021 [1]. Mutations affect evolutionary conservation of microorganisms. The emergence of new variants is an expected occurrence as it has been the case of SARS-CoV-2. A variation of SARS-CoV-2 due to evolution and adaptation processes has been detected globally. While most emerging mutations will not have significant impact on the spread of the virus, some mutations or combinations of mutations may provide the virus with a selective advantage, such as increased transmissibility or the ability to evade the host immune response. In that instances, the variants could increase the risk to human health and are considered to be variants of concern (VOC) [2].

Since the outbreak of COVID-19 pandemic, new SARS-CoV-2 variants have been reported from the United Kingdom, France, South Africa, Denmark, and Nigeria [2,3]. The fast pace evolutionary changes are currently affecting pathogenicity of SARS-CoV-2 as the third-wave slams the global communities, and this called for urgent in silico, in vitro, and in vivo studies [4,5]. According to Huang et al. [6], SARS-CoV-2 protein mutations have two imperative features: (i) a higher ability to infect and enhanced pathogenicity than the bat-like SARS-CoV, and (ii) a lower pathogenicity than SARS-CoV. It has been reported that the existing approved vaccines which include two mRNA-based anti-SARS-CoV-2 vaccines; BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna), as well as three inactivated virus-based vaccines; BBIBP-CorV vaccine (Sinopharm), BBV152 (Bharat Biotech International Limited), and CoronaVac (Sinovac Biotech), were significantly less protective against Beta variant of coronavirus [7].

The World Health Organization (WHO) has provided new nomenclature for VOC on 31 May 2021 using Greek letters: Alpha for B.1.1.7; Beta for B.1.351; Gamma for P.1; Delta for B.1.617.2, and others. Beta variant (B.1.351 VOC-20DEC-02 (VOC-202012/02), GH/501Y.V2) of coronavirus is characterized by 17 mutations, which are: eight spike protein mutations (D80A, D215G, 241/243 deletion, K417N, E484K, N501Y, D614G, and A701V), four open reading frame 1a (orf1a) mutations, one orflb mutation, one nucleocapsid (N) protein mutation and three others [8]. RNA-dependent RNA polymerase (RdRp) is one of the non-structural proteins (NSPs) derived from the polyprotein encoded ORF1 of SARS-CoV-2 [9]. Non-structural protein (nsp) of SARS-CoV-2 which include 3-Chymotrypsin-like protease (3CL^pro), Papain-like protease (PL^pro), helicase (nsp13), RdRp (nsp12), 2’-O-ribose methyltransferase (nsp16) has been investigated computationally, as potential targets for therapeutic discovery [10]. V843F and A889V are the two mutations reported for PLPro, with V843F mutation being the most prevalent mutation in the clinical samples [11]. It has been reported that PLpro (PDB ID: 5Y3E) is less deformed and could be less susceptible during viral mutations [10]. In silico approach has been used to compare annotated functional domains of SARS-CoV and SARS-CoV-2 sequences. An in silico molecular dynamics study on the protein structure was used to predict amino acid residues T478K mutation in Spike protein and that might significantly alter the electrostatic surface of the protein and their binding with human receptor angiotensin-converting enzyme 2 (ACE2) as well as prevention and curative measures such as vaccines, antiviral drugs, and monoclonal antibodies [12]. In this study, the structural fluctuations of the amino acid residues in the spike glycoprotein and nsp12 of SARS-CoV-2 were investigated by in silico approach to decipher susceptibility to mutation.

The result of this study showed that RNA-dependent RNA polymerase (nsp12) with amino acid residues (rmsf) 40 (3.00 Å), 50 (3.79 Å), 119 (4.56 Å), 120 (3.53 Å), 220 (3.84 Å), 263 (3.33 Å), 265 (4.31 Å), 270 (3.30 Å), and 499 (3.00 Å) could be very susceptible to mutation as shown in figure 1. The result of this study showed that spike glycoprotein with amino acid residues (rmsf) 282 (3.65 Å), 477 (4.21 Å), 478 (4.82 Å), 479 (5.40 Å), 481 (5.94 Å), 560 (4.63 Å), 703 (3.94 Å), 704 (4.02 Å), 848 (4.58 Å), 1041 (3.94 Å), 1144 (4.56 Å) and 1147 (4.61 Å) could be very susceptible to mutation as shown in figure 2.

FIGURE 1

FIGURE 2

The SAR-CoV-2 mutations destabilized the overall protein structure in multiples of amino acid residues which could interfere with active site leading to insensitivity or resistance to the inhibitors as seen in Figure 1C and 2C. Mutation T478K of Spike glycoprotein showed the highest deviation in the structure while other mutations seem to limitedly affected the structure.

The results of comparison of protein sequences SARS-CoV-2 and SARS-CoV by Blastp, has shown that orf8 and orf10 proteins were not present in SARS-CoV, while surface glycoprotein, nsp2, nsp3, orf3a, and orf6 proteins, have percent identity of less than 80% of variation between SARS-CoV-2 and SARS-CoV [16]. According to the alignment analysis, the closest similarity was between the two COVID-19 genomes (99%) compared with the two bat CoV [4]. The orf1a polyprotein of SARS-CoV-2 is similar to that SARS-CoV by 80.58% identity [16]. Spike glycoprotein Receptor-Binding Domain (RBD; aa 319-541), has vital functional and antigenic properties, and any mutation in this region has potential for reduced susceptibility to neutralizing antibodies elicited by vaccination or prior infection [17].

D614G mutation in spike glycoprotein and P323L in RNA-dependent RNA polymerase (nsp12) are the globally dominant variants with a high frequency [14]. Variant of Nextstrain cluster 20A.EU2 has been reported with mutation of S477N in spike protein of the new SARS-CoV-2, which was rapidly increased in France at the start of the second wave, probably due to initiation effects, and prevalent also in Belgium, Czech, Denmark, Hungary, Netherlands, and Switzerland [18]. The P681H mutation is also characteristic of the new SARS-CoV-2 variants from the United Kingdom and Nigeria [3].

A recent report on the distribution of the Spike mutation S:T478K and its recent growth in prevalence in the SARS-CoV-2 population of Mexico, United States, and several European countries, showed that S:T478K is frequently co-occurring with three other Spike mutations; D614G, P681H and T732A, with 99.83%, 93.8% and 88.7% co-occurrence respectively as well as two amino acid residues mutation in Nucleocapsid (N:RG203KR), and mutations in nsp12 [9]. Moreover, bioinformatics study has predicted G476S, and T478I mutation in spike glycoprotein and G25Y, G228C, V330E, L810H and D824Y in nsp12 [14]. A study has reported that mutations in 2891, 3036, 14408, 23403 and 28881 positions of SARS-CoV-2 genomic sequence, are predominantly observed in Europe, whereas those located at positions 17746, 17857 and 18060 are exclusively present in North America [19]. These mutations were belonged to the sequence of ORF1ab (1397 nsp2, 2891 nsp3, 14408 nsp12 (RdRp), 17746 and 17857 nsp143, 18060 nsp14), S (23403, spike protein) and ORF9a (28881, nucleocapsid phosphoprotein), respectively [19]. Interestingly, the docking site for inhibitors is not within the catalytic domain of the RdRp [10] but the docking site for inhibitors of the spike glycoprotein is on the Receptor-Binding Domain in the N-terminal region of S1 which is responsible for viral attachment to target cells via the ACE2 receptor [17,20].

The VOC B.1.1.529 (Omicron) belongs to Pango lineage B.1.1.529, Nextstrain clade 21K, is the most divergent variant, and characterized by 30 amino acid substitutions, 3 deletions and one insertion in the spike protein compared to the original virus (A67V, del69-70, T95I, del142-144, Y145D, del211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F) [21]. Most of the substitutions in the sequence coding the spike protein have been found associated with almost complete escape from neutralization by convalescent and vaccinee sera [22].

This study has shown key amino acid residues of SARS-CoV-2 spike glycoprotein and nsp12 that could be susceptibility to mutation. Overall, spike glycoprotein has highest number of mutations and these variants could increase the risk to human health if not mitigated in the population. Consequently, it is imperative to investigate and characterize SARS-CoV-2 spike glycoprotein and nsp12 (RdRp) mutation in order to assess possible drug-resistance viral phenotypes. However, based on the existing classification, these variants may not be of interest or high consequence, in that currently no coherent proof that efficacy of prevention and curative measures such as vaccines, antiviral drugs, and monoclonal antibodies, are significantly decreased in comparison to earlier perpetrating variants [21,23]. As of 1 December 2021, a total of 7,885,790,810 vaccine doses have been administered globally [1]. Thus, there should be concerted efforts toward administration and development of holistic vaccines that will directly target the existing and emergent variants of SARS-CoV-2.